@genome-spy/core 0.40.0 → 0.42.0

package/dist/src/utils/binnedIndex.js

@@ -15,6 +15,8 @@ const MIN_INTEGER = -(2 ** 31);
  * A binned index for (overlapping) ranges that are sorted by their start position.
  * Each indexed range is associated with respective vertex indices.
  *
+ * The indexing scheme is somewhat similar to Tabix (https://academic.oup.com/bioinformatics/article/27/5/718/262743).
+ *
  * @param {number} size Number of bins
  * @param {[number, number]} domain Domain of positions
  * @param {(datum: T) => number} accessor Accessor for range's start position
@@ -27,13 +29,15 @@ export function createBinningRangeIndexer(
     accessor,
     accessor2 = accessor
 ) {
-    const startIndices = new Int32Array(size);
+    const startIndices = new Array(size);
     startIndices.fill(MAX_INTEGER);
 
     let lastIndex = MIN_INTEGER;
+    let lastStart = -Infinity;
     let unordered = false;
 
-    const endIndices = new Int32Array(size);
+    const endIndices = new Array(size);
+    endIndices.fill(0);
 
     const start = domain[0];
     const domainLength = domain[1] - domain[0];
@@ -63,17 +67,33 @@ export function createBinningRangeIndexer(
      * @param {number} endVertexIndex
      */
     function binningIndexer(datum, startVertexIndex, endVertexIndex) {
+        if (unordered) {
+            return;
+        }
+
         if (startVertexIndex > lastIndex) {
             lastIndex = startVertexIndex;
-        } else if (!unordered) {
+        } else {
             unordered = true;
             // TODO: Contextual info like view path
             console.debug(
                 "Items are not ordered properly. Disabling binned index."
             );
+            return;
         }
 
         const value = accessor(datum);
+
+        if (value < lastStart) {
+            unordered = true;
+            // TODO: Contextual info like view path
+            console.debug(
+                "Items are not ordered properly. Disabling binned index."
+            );
+            return;
+        }
+        lastStart = value;
+
         const bin = getBin(value, false);
 
         if (startIndices[bin] > startVertexIndex) {
@@ -93,18 +113,42 @@ export function createBinningRangeIndexer(
      * @param {number} endVertexIndex
      */
     function binningRangeIndexer(datum, startVertexIndex, endVertexIndex) {
+        if (unordered) {
+            return;
+        }
+
         if (startVertexIndex > lastIndex) {
             lastIndex = startVertexIndex;
-        } else if (!unordered) {
+        } else {
             unordered = true;
             // TODO: Contextual info like view path
             console.debug(
-                "Items are not ordered properly. Disabling binned index."
+                "Items (vertices) are not ordered properly. Disabling binned index."
             );
+            return;
         }
 
         const start = accessor(datum);
         const end = accessor2(datum);
+
+        if (start < lastStart) {
+            unordered = true;
+            // TODO: Contextual info like view path
+            console.debug(
+                "Items are not ordered properly. Disabling binned index."
+            );
+            return;
+        } else if (end < start) {
+            unordered = true;
+            // TODO: Contextual info like view path
+            console.debug(
+                "End index is less than start index. Disabling binned index. Datum: ",
+                datum
+            );
+            return;
+        }
+        lastStart = start;
+
         const startBin = getBin(start, false);
         const endBin = getBin(end, true);
 
@@ -135,7 +179,16 @@ export function createBinningRangeIndexer(
         return arr;
     };
 
+    /**
+     * Finalizes the index and returns a lookup function.
+     *
+     * @returns {Lookup}
+     */
     const getIndex = () => {
+        if (unordered) {
+            return undefined;
+        }
+
         for (let i = 1; i < endIndices.length; i++) {
             if (endIndices[i] < endIndices[i - 1]) {
                 endIndices[i] = endIndices[i - 1];
@@ -159,9 +212,5 @@ export function createBinningRangeIndexer(
     binningIndexer.getIndex = getIndex;
     binningRangeIndexer.getIndex = getIndex;
 
-    if (unordered) {
-        return undefined;
-    } else {
-        return accessor == accessor2 ? binningIndexer : binningRangeIndexer;
-    }
+    return accessor == accessor2 ? binningIndexer : binningRangeIndexer;
 }

package/dist/src/utils/binnedIndex.test.js

@@ -152,4 +152,50 @@ describe("Binning Indexer", () => {
         expect(index(115, 116)).toEqual([4, 8]);
         expect(index(135, 145)).toEqual([6, 10]);
     });
+
+    test("Unordered ranges disable the index", () => {
+        const items = [
+            [10, 30],
+            [25, 50],
+
+            [112, 139],
+            [102, 129], // <- Unordered!
+            [121, 149],
+        ];
+        const indexer = createBinningRangeIndexer(
+            100,
+            [0, 1000],
+            (x) => x[0],
+            (x) => x[1]
+        );
+
+        items.forEach((x, i) => indexer(x, i * 2, (i + 1) * 2));
+
+        const index = indexer.getIndex();
+
+        expect(index).toBeUndefined();
+    });
+
+    test("Inverted ranges disable the index", () => {
+        const items = [
+            [10, 30],
+            [25, 50],
+
+            [102, 129],
+            [139, 112], // <- Inverted!
+            [121, 149],
+        ];
+        const indexer = createBinningRangeIndexer(
+            100,
+            [0, 1000],
+            (x) => x[0],
+            (x) => x[1]
+        );
+
+        items.forEach((x, i) => indexer(x, i * 2, (i + 1) * 2));
+
+        const index = indexer.getIndex();
+
+        expect(index).toBeUndefined();
+    });
 });

package/dist/src/utils/expression.d.ts

@@ -1,9 +1,19 @@
 /**
+ * @typedef { object } ExpressionProps
+ * @prop { string[] } fields
+ * @prop { string[] } globals
+ * @prop { string } code
+ *
+ * @typedef { ((x: object) => any) & ExpressionProps } ExpressionFunction
  *
  * @param {string} expr
+ * @returns {ExpressionFunction}
  */
-export default function createFunction(expr: string, globalObject?: {}): {
-    (x: object): any;
+export default function createFunction(expr: string, globalObject?: {}): ExpressionFunction;
+export type ExpressionProps = {
     fields: string[];
+    globals: string[];
+    code: string;
 };
+export type ExpressionFunction = ((x: object) => any) & ExpressionProps;
 //# sourceMappingURL=expression.d.ts.map

package/dist/src/utils/expression.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"expression.d.ts","sourceRoot":"","sources":["../../../src/utils/expression.js"],"names":[],"mappings":"AAEA;;;GAGG;AACH,6CAFW,MAAM;QAqBwB,MAAM;;EAO9C"}
+{"version":3,"file":"expression.d.ts","sourceRoot":"","sources":["../../../src/utils/expression.js"],"names":[],"mappings":"AAyDA;;;;;;;;;;GAUG;AACH,6CAHW,MAAM,sBACJ,kBAAkB,CAyB9B;;YAhCU,MAAM,EAAE;aACR,MAAM,EAAE;UACR,MAAM;;sCAEE,MAAM,KAAK,GAAG"}

package/dist/src/utils/expression.js

@@ -1,17 +1,72 @@
-import { parseExpression, codegenExpression } from "vega-expression";
+import { parseExpression, codegenExpression, functions } from "vega-expression";
+import {
+    isArray,
+    isBoolean,
+    isNumber,
+    isObject,
+    isRegExp,
+    isString,
+    lerp,
+} from "vega-util";
+import smoothstep from "./smoothstep.js";
+import clamp from "./clamp.js";
+import linearstep from "./linearstep.js";
 
 /**
+ * Some bits are adapted from https://github.com/vega/vega/blob/main/packages/vega-functions/src/codegen.js
+ */
+const functionContext = {
+    clamp,
+    isArray,
+    isBoolean,
+    isDefined(/** @type {any} */ _) {
+        return _ !== undefined;
+    },
+    isNumber,
+    isObject,
+    isRegExp,
+    isString,
+    isValid(/** @type {any} */ _) {
+        // eslint-disable-next-line no-self-compare
+        return _ != null && _ === _;
+    },
+    lerp,
+    linearstep,
+    smoothstep,
+};
+
+/**
+ * @param {typeof codegenExpression} codegen
+ */
+function buildFunctions(codegen) {
+    const fn = functions(codegen);
+    // eslint-disable-next-line guard-for-in
+    for (const name in functionContext) {
+        fn[name] = `this.${name}`;
+    }
+    return fn;
+}
+
+const cg = codegenExpression({
+    forbidden: [],
+    allowed: ["datum"],
+    globalvar: "globalObject",
+    fieldvar: "datum",
+    functions: buildFunctions,
+});
+
+/**
+ * @typedef { object } ExpressionProps
+ * @prop { string[] } fields
+ * @prop { string[] } globals
+ * @prop { string } code
+ *
+ * @typedef { ((x: object) => any) & ExpressionProps } ExpressionFunction
  *
  * @param {string} expr
+ * @returns {ExpressionFunction}
  */
 export default function createFunction(expr, globalObject = {}) {
-    const cg = codegenExpression({
-        forbidden: [],
-        allowed: ["datum"],
-        globalvar: "globalObject",
-        fieldvar: "datum",
-    });
-
     try {
         const parsed = parseExpression(expr);
         const generatedCode = cg(parsed);
@@ -21,11 +76,15 @@ export default function createFunction(expr, globalObject = {}) {
             "datum",
             "globalObject",
             `"use strict"; return (${generatedCode.code});`
-        );
+        ).bind(functionContext);
 
+        /** @type { ExpressionFunction } */
         const exprFunction = /** @param {object} x */ (x) =>
             fn(x, globalObject);
         exprFunction.fields = generatedCode.fields;
+        exprFunction.globals = generatedCode.globals;
+        exprFunction.code = generatedCode.code;
+
         return exprFunction;
     } catch (e) {
         throw new Error(`Invalid expression: ${expr}, ${e.message}`);

package/dist/src/utils/linearstep.d.ts

@@ -0,0 +1,7 @@
+/**
+ * @param {number} edge0
+ * @param {number} edge1
+ * @param {number} x
+ */
+export default function linearstep(edge0: number, edge1: number, x: number): number;
+//# sourceMappingURL=linearstep.d.ts.map

package/dist/src/utils/linearstep.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"linearstep.d.ts","sourceRoot":"","sources":["../../../src/utils/linearstep.js"],"names":[],"mappings":"AAEA;;;;GAIG;AACH,0CAJW,MAAM,SACN,MAAM,KACN,MAAM,UAIhB"}

package/dist/src/utils/linearstep.js

@@ -0,0 +1,10 @@
+import clamp from "./clamp.js";
+
+/**
+ * @param {number} edge0
+ * @param {number} edge1
+ * @param {number} x
+ */
+export default function linearstep(edge0, edge1, x) {
+    return clamp((x - edge0) / (edge1 - edge0), 0.0, 1.0);
+}

package/dist/src/view/gridView.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"gridView.d.ts","sourceRoot":"","sources":["../../../src/view/gridView.js"],"names":[],"mappings":"AAowBA;;;GAGG;AACH,iDAHW,OAAO,iBAAiB,EAAE,cAAc,GACtC,OAAO,iBAAiB,EAAE,QAAQ,CAwB9C;AAED;;;GAGG;AACH,uDAHW,OAAO,iBAAiB,EAAE,cAAc,GACtC,OAAO,iBAAiB,EAAE,QAAQ,CA6C9C;AA2BD;;GAEG;AACH,8EAUC;AAED;;;;;GAKG;AACH,4CAJW,OAAO,uBAAuB,EAAE,OAAO,UACvC,OAAO,iBAAiB,EAAE,UAAU,YACpC,QAAQ,aAmBlB;AA33BD;;;;;;;;;;;;;;;GAeG;AACH;IA6BI;;;;;;;;;OASG;IACH,kBARW,OAAO,iBAAiB,EAAE,aAAa,WACvC,OAAO,yBAAyB,EAAE,OAAO,gBACzC,aAAa,iDAEb,MAAM,WACN,MAAM,YACN,OAAO,WAAW,EAAE,WAAW,EAoBzC;IARG,8CAAgB;IAOhB,uBAA0B;IAG9B;;OAEG;IACH,qDAIC;IAeD;;OAEG;IACH,wDAKC;IAqBD;;OAEG;IACH,8CAEC;IAED,yBAEC;IAED;;OAEG;IACH,wCAmCC;IA2OD;;;;OAIG;IAEH,gBALW,OAAO,4CAA4C,EAAE,OAAO,UAC5D,OAAO,uBAAuB,EAAE,OAAO,YACvC,OAAO,uBAAuB,EAAE,gBAAgB,QA6O1D;;CAmGJ;AAgJD;IACI;;;;OAIG;IACH,6DAHW,aAAa,UACb,MAAM,EAoFhB;IAjFG,4BAAgC;IAChC,kCAAgB;IAChB,eAAoB;IAEpB,uBAAuB;IACvB,YADW,QAAQ,CACQ;IAE3B,uBAAuB;IACvB,kBADW,QAAQ,CACc;IAEjC,mFAAmF;IACnF,MADW,QAAQ,OAAO,OAAO,iBAAiB,EAAE,UAAU,EAAE,QAAQ,CAAC,CAAC,CAC5D;IAEd,4FAA4F;IAC5F,WADW,QAAQ,OAAO,OAAO,iBAAiB,EAAE,UAAU,EAAE,YAAY,CAAC,CAAC,CAC3D;IAEnB,0DAA0D;IAC1D,kEAAoB;IAEpB,uBAAuB;IACvB,OADW,QAAQ,CACG;IAEtB,wBAAwB;IACxB,QADW,SAAS,CACQ;IA4DhC,uEAcC;IAED;;OAEG;IACH,4BAkKC;IAED,uBAqBC;IAED,iCAEC;CACJ;qBAhrC0D,eAAe;sBAFpD,uBAAuB;0BAGnB,oBAAoB;qBAGzB,eAAe;yBALX,mBAAmB;AAmrC5C;IACI;;;OAGG;IACH,uBAHW,SAAS,8CAyFnB;IAtDG;;;MAAoB;IACpB,2CAAsC;IAKtC,uBAAuB;IAEvB,wBAAwB;IACxB,2BAAqC;IA+CzC,0BAKC;IAWD;;;;OAIG;IACH,gCAHW,SAAS,UACT,SAAS,QA8CnB;IA7BG,0BAAsE;CA8B7E;oBAp1CmB,qBAAqB"}

package/dist/src/view/gridView.js

@@ -436,6 +436,8 @@ export default class GridView extends ContainerView {
      */
     // eslint-disable-next-line complexity
     render(context, coords, options = {}) {
+        super.render(context, coords, options);
+
         if (!this.isConfiguredVisible()) {
             return;
         }

package/dist/src/view/layerView.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"layerView.d.ts","sourceRoot":"","sources":["../../../src/view/layerView.js"],"names":[],"mappings":"AAIA;IAQI;;;;;;;;OAQG;IACH,kBAPW,OAAO,iBAAiB,EAAE,SAAS,WACnC,OAAO,yBAAyB,EAAE,OAAO,gBACzC,aAAa,cACb,OAAO,WAAW,EAAE,OAAO,QAC3B,MAAM,YACN,OAAO,WAAW,EAAE,WAAW,EAQzC;IAHG,0CAAgB;IAoCpB,gEAEC;IAWD;;;;OAIG;IACH,gBAJW,OAAO,4CAA4C,EAAE,OAAO,UAC5D,OAAO,uBAAuB,EAAE,OAAO,YACvC,OAAO,uBAAuB,EAAE,gBAAgB,QAc1D;;CAeJ;0BAxGyB,oBAAoB"}
+{"version":3,"file":"layerView.d.ts","sourceRoot":"","sources":["../../../src/view/layerView.js"],"names":[],"mappings":"AAIA;IAQI;;;;;;;;OAQG;IACH,kBAPW,OAAO,iBAAiB,EAAE,SAAS,WACnC,OAAO,yBAAyB,EAAE,OAAO,gBACzC,aAAa,cACb,OAAO,WAAW,EAAE,OAAO,QAC3B,MAAM,YACN,OAAO,WAAW,EAAE,WAAW,EAQzC;IAHG,0CAAgB;IAoCpB,gEAEC;IAWD;;;;OAIG;IACH,gBAJW,OAAO,4CAA4C,EAAE,OAAO,UAC5D,OAAO,uBAAuB,EAAE,OAAO,YACvC,OAAO,uBAAuB,EAAE,gBAAgB,QAgB1D;;CAeJ;0BA1GyB,oBAAoB"}

package/dist/src/view/layerView.js

@@ -77,6 +77,8 @@ export default class LayerView extends ContainerView {
      * @param {import("../types/rendering.js").RenderingOptions} [options]
      */
     render(context, coords, options = {}) {
+        super.render(context, coords, options);
+
         if (!this.isConfiguredVisible()) {
             return;
         }

package/dist/src/view/unitView.d.ts

@@ -28,12 +28,6 @@ export default class UnitView extends ContainerView {
     spec: import("../spec/view.js").UnitSpec;
     /** @type {import("../marks/mark.js").default} */
     mark: import("../marks/mark.js").default;
-    /**
-     * Not nice! Inconsistent when faceting!
-     * TODO: Something. Maybe store only width/height
-     * @type {import("./layout/rectangle.js").default}
-     */
-    coords: import("./layout/rectangle.js").default;
     /**
      * @param {import("./renderingContext/viewRenderingContext.js").default} context
      * @param {import("./layout/rectangle.js").default} coords

package/dist/src/view/unitView.d.ts.map

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+{"version":3,"file":"unitView.d.ts","sourceRoot":"","sources":["../../../src/view/unitView.js"],"names":[],"mappings":"AAqBA;;;;GAIG;AACH;QAHkB,MAAM,GAAE,cAAc,kBAAkB,EAAE,OAAO;EASjE;AAEF;IACI;;;;;;;OAOG;IACH;;;;;;;;OAQG;IACH,kBAPW,OAAO,iBAAiB,EAAE,QAAQ,WAClC,OAAO,yBAAyB,EAAE,OAAO,gBACzC,OAAO,oBAAoB,EAAE,OAAO,cACpC,OAAO,WAAW,EAAE,OAAO,QAC3B,MAAM,YACN,OAAO,WAAW,EAAE,WAAW,EAkBzC;IAbG,yCAAgB;IAIZ,iDAAiD;IACjD,MADW,OAAO,kBAAkB,EAAE,OAAO,CACnB;IAUlC;;;;OAIG;IACH,gBAJW,OAAO,4CAA4C,EAAE,OAAO,UAC5D,OAAO,uBAAuB,EAAE,OAAO,YACvC,OAAO,uBAAuB,EAAE,gBAAgB,QAY1D;IAED,kDAIC;IAED;;;;;OAKG;IACH,iEAyEC;IAED;;;OAGG;IACH,mGASC;IAkBD;;OAEG;IACH,uDAEC;IAED;;OAEG;IACH,opBAcC;IAED;;;;;OAKG;IACH,6BAHW,OAAO,oBAAoB,EAAE,gBAAgB,iDAkBvD;IAED;;;;;;;;;;;;OAYG;IACH,gHA2CC;IAED,uBAQC;IAgBD;;;;OAIG;IACH,8BAJW,MAAM,+DAEJ,OAAO,iBAAiB,EAAE,kBAAkB,CAKxD;CACJ;0BAnVyB,oBAAoB"}

package/dist/src/view/unitView.js

@@ -65,13 +65,6 @@ export default class UnitView extends ContainerView {
 
         this.resolve();
 
-        /**
-         * Not nice! Inconsistent when faceting!
-         * TODO: Something. Maybe store only width/height
-         * @type {import("./layout/rectangle.js").default}
-         */
-        this.coords = undefined;
-
         this.needsAxes = { x: true, y: true };
     }
 
@@ -81,12 +74,12 @@ export default class UnitView extends ContainerView {
      * @param {import("../types/rendering.js").RenderingOptions} [options]
      */
     render(context, coords, options = {}) {
+        super.render(context, coords, options);
+
         if (!this.isConfiguredVisible()) {
             return;
         }
 
-        this.coords = coords;
-
         context.pushView(this, coords);
         context.renderMark(this.mark, options);
         context.popView(this);

package/dist/src/view/view.d.ts

@@ -46,6 +46,12 @@ export default class View {
      * @type {function(number):number}
      */
     opacityFunction: (arg0: number) => number;
+    /**
+     * Not nice! Inconsistent when faceting!
+     * TODO: Something. Maybe store only width/height
+     * @type {import("./layout/rectangle.js").default}
+     */
+    coords: import("./layout/rectangle.js").default;
     context: import("../types/viewContext.js").default;
     layoutParent: import("./containerView.js").default;
     dataParent: View;

package/dist/src/view/view.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"view.d.ts","sourceRoot":"","sources":["../../../src/view/view.js"],"names":[],"mappings":"AAyBA,oBAAoB;AACpB,sCAAuC;AACvC,0BAA0B;AAC1B,sCAAuC;AAKvC;;;;;;;;;;;;;;;;;;;;;;;;;;;GA2BG;AACH;IAsBI;;;;;;;;;OASG;IACH,kBARW,OAAO,iBAAiB,EAAE,QAAQ,WAClC,OAAO,yBAAyB,EAAE,OAAO,gBACzC,OAAO,oBAAoB,EAAE,OAAO,cACpC,OAAO,WAAW,EAAE,OAAO,QAC3B,MAAM,YACN,WAAW,EAwCrB;IA3DD;;OAEG;IACH,wBAFmB,MAAM,KAAE,MAAM,CAEQ;IAEzC;;;;OAIG;IACH,QAFU,OAAO,uBAAuB,EAAE,OAAO,CAE1C;IAiBH,mDAAsB;IACtB,mDAAgC;IAChC,iBAA4B;IAC5B,aAA6B;IAC7B,yCAAgB;IAEhB;QACI;;;WAGG;eADO,QAAQ,OAAO,OAAO,oBAAoB,EAAE,gBAAgB,EAAE,OAAO,sBAAsB,EAAE,OAAO,CAAC,CAAC;QAGhH;;;WAGG;cADO,QAAQ,OAAO,OAAO,oBAAoB,EAAE,wBAAwB,EAAE,OAAO,qBAAqB,EAAE,OAAO,CAAC,CAAC;MAG1H;IAID;;;;kCA/DE,OAAO;;;;kCAEP,OAAO;MAiER;IAED;;;OAGG;IACH,WAFU,OAAO,OAAO,oBAAoB,EAAE,wBAAwB,EAAE,OAAO,CAAC,CAEzC;IAG3C,sBAIC;IAED;;;;OAIG;IACH,eAFa,OAAO,CAInB;IAED;;;;;OAKG;IACH,gBAFa,OAAO,CAMnB;IAED;;;;;OAKG;IACH,WAFa,cAAc,CAW1B;IAED;;OAEG;IACH,mBAFa,cAAc,CAkB1B;IAoED,+BAEC;IAED,2BAEC;IAED;;;;;;;;OAQG;IACH,aAFa,OAAO,CAMnB;IAED;;;;;;;OAOG;IACH,uBAFa,MAAM,CAMlB;IAED,wBAKC;IAkBD;;OAEG;IACH,6BAEC;IAED;;OAEG;IACH,2BAEC;IAED;;;;OAIG;IACH,yBAFW,gBAAgB,QAO1B;IAED;;;;OAIG;IACH,2BAHW,MAAM,kBACG,gBAAgB,KAAE,IAAI,QASzC;IAED;;;;;;;OAOG;IACH,+BALW,OAAO,uBAAuB,EAAE,OAAO,SAEvC,OAAO,8BAA8B,EAAE,OAAO,aAC9C,OAAO,QASjB;IAED;;;;;;;;;;OAUG;IACH,kCAJW,MAAM,YACN,wBAAwB,eACxB,OAAO,QAajB;IAED;;;;;;;OAOG;IACH,eAJW,OAAO,GACL,WAAW,CAmBvB;IAED;;OAEG;IACH,yBAOC;IAED;;OAEG;IACH,6BASC;IAED;;;OAGG;IACH,uBAEC;IApayB,yJAIN;IAgbpB;;;;;;OAMG;IACH,eAFY,OAAO,oBAAoB,EAAE,QAAQ,CAuBhD;IAED;;;;OAIG;IACH,+BAJW,IAAI,UAEM,MAAM,KAAE,GAAG,CAM/B;IAED;;;;;OAKG;IACH,6BAHW,IAAI,GACF,MAAM,EAAE,CASpB;IAED;;;;;;;;;;;;;;;OAeG;IACH,yBAFY,YAAY,CAIvB;IAED;;OAEG;IACH,4BAFW,OAAO,oBAAoB,EAAE,gBAAgB,0CAWvD;IAED;;OAEG;IACH,2BAFW,OAAO,oBAAoB,EAAE,iBAAiB,yCAWxD;IAED;;;;OAIG;IACH,iCAJW,OAAO,oBAAoB,EAAE,OAAO,GAAG,SAAS,kBAChD,OAAO,iBAAiB,EAAE,gBAAgB,GACxC,OAAO,iBAAiB,EAAE,kBAAkB,CAIxD;IAED;;;;OAIG;IACH,0CAJW,OAAO,oBAAoB,EAAE,OAAO,kBACpC,OAAO,iBAAiB,EAAE,gBAAgB,GACxC,OAAO,iBAAiB,EAAE,kBAAkB,CAQxD;IAED;;;;OAIG;IACH,8BAJW,OAAO,oBAAoB,EAAE,OAAO,kBACpC,OAAO,iBAAiB,EAAE,gBAAgB,GACxC,OAAO,iBAAiB,EAAE,kBAAkB,CAIxD;IAED;;OAEG;IACH,cAFa,MAAM,CAOlB;IAED;;OAEG;IACH,8BAEC;IAED,uBAKC;IAED;;;;;;OAMG;IACH,yBANW,GAAG,wCAQb;IAED;;;;OAIG;IACH,8BAHW,MAAM,cACN,MAAM,GAAG,SAAS,GAAG,WAAW,QAiB1C;IAED,4BAEC;IAED;;;;;OAKG;IACH,iCAFW,OAAO,8BAA8B,EAAE,OAAO,QAIxD;;CACJ;AAqEM,iCAHI,GAAG,0CAGkC;0BA9sBnC,8BAAsB,IAAI;qCAG5B,IAAI,KACF,WAAW;sBAEX,eAAe,GAAG;IAC9B,SAAgB,CAAC,SAAW,IAAI,KAAE,IAAI,CAAC;IACvC,cAAqB,CAAC,SAAW,IAAI,KAAE,IAAI,CAAC;IAC5C,aAAoB,CAAC,SAAW,IAAI,KAAE,IAAI,CAAA;CAAC;;;;;UAIlC,OAAO,iBAAiB,EAAE,kBAAkB;;;;cAC5C,GAAG;;gDAGF,OAAO,uBAAuB,EAAE,OAAO,SAEvC,OAAO,8BAA8B,EAAE,OAAO;;;;;+BAG/C,OAAO;;;;+BAEP,OAAO;;oBArDG,qBAAqB;+BADlC,wBAAwB"}

package/dist/src/view/view.js

@@ -16,6 +16,7 @@ import { appendToBaseUrl } from "../utils/url.js";
 import { isDiscrete, bandSpace } from "vega-scale";
 import { peek } from "../utils/arrayUtils.js";
 import ViewError from "./viewError.js";
+import { isExprRef } from "../marks/mark.js";
 
 // TODO: View classes have too many responsibilities. Come up with a way
 // to separate the concerns. However, most concerns are tightly tied to
@@ -73,6 +74,13 @@ export default class View {
      */
     opacityFunction = defaultOpacityFunction;
 
+    /**
+     * Not nice! Inconsistent when faceting!
+     * TODO: Something. Maybe store only width/height
+     * @type {import("./layout/rectangle.js").default}
+     */
+    coords;
+
     /**
      *
      * @param {import("../spec/view.js").ViewSpec} spec
@@ -461,6 +469,10 @@ export default class View {
      * @type {import("../types/rendering.js").RenderMethod}
      */
     render(context, coords, options = {}) {
+        this.coords = options.clipRect
+            ? coords.intersect(options.clipRect)
+            : coords;
+
         // override
     }
 
@@ -723,6 +735,11 @@ function createViewOpacityFunction(view) {
 
                 return interpolate(unitsPerPixel) * parentOpacity;
             };
+        } else if (isExprRef(opacityDef)) {
+            const fn = view.context.paramBroker.createExpression(
+                opacityDef.expr
+            );
+            return (parentOpacity) => fn(null) * parentOpacity;
         }
     }
     return (parentOpacity) => parentOpacity;

package/package.json

@@ -7,7 +7,7 @@
   },
   "contributors": [],
   "license": "MIT",
-  "version": "0.40.0",
+  "version": "0.42.0",
   "jsdelivr": "dist/bundle/index.js",
   "unpkg": "dist/bundle/index.js",
   "browser": "dist/bundle/index.js",
@@ -42,7 +42,7 @@
     "@gmod/bgzf-filehandle": "^1.4.7",
     "@gmod/gff": "^1.3.0",
     "@gmod/indexedfasta": "^2.0.4",
-    "@gmod/tabix": "^1.5.10",
+    "@gmod/tabix": "^1.5.13",
     "@types/d3-array": "^3.0.2",
     "@types/d3-dsv": "^3.0.0",
     "@types/d3-ease": "^3.0.0",
@@ -65,5 +65,5 @@
     "vega-scale": "^7.1.1",
     "vega-util": "^1.16.0"
   },
-  "gitHead": "74d4f6721b31c1916051f868e95be7d83d8d6369"
+  "gitHead": "59a4384ba903ee1b81212593e872ea61accc729d"
 }